So it turns out it was a combination of things.
For one, I had the wrong name for the bios file and flash file.
Two, the bios files I had did not match the recalbox md5 checksums (although I never found a checksum that matched for the dc_flash.bin file).
And finally, apparently the bios files need to go into the actual system folder and not the folder labeled "bios" (although I put them in both locations).
So far it played every image I put on it and they ran at anywhere from semi playable to playable at stock speeds on the pi3. Overclocking to 1350 yielded slightly better performance. The emulator still has a ways to go though.
For anyone looking for the correct md5 hashes you can go here, it will also tell you the correct name and location for your bios files.